出る釘は主役を演じる
When my brother was home for Spring Break this year and playing Ogre Battle 64, I realized that it was yet another Japanese video game where the hero deserts the evil empire and joins the resistance. I thought that this seemed odd, considering how traditional and conformist Japanese society is (although it's starting to change). I guess that's a sign that fiction is a radical, non-mainstream element of society. Just to illustrate this, I decided to list a bunch of adventure stories I knew from modern media and see how they add up. Hopefully I wasn't too biased in which ones came to mind.
For these purposes, "establishment" is the main power in the setting, whether it's the most powerful nation, the state religion, the secret society behind the throne, the student council, the local gang, super-powerful invading aliens, God, destiny, or whatever. Where the protagonists' motives change throughout the story, I list the one that they choose in the end (as far as I've seen). Where there are multiple paths, I list the main one. Where the series has more than one separate storyline, I hope I've listed which I mean. Where I couldn't decide (for instance, in SIMOUN, where it's a war between as-far-as-I-know two equally powerful nations), I've left them out. I've also recused (?) sentai and mahō shōjo shows, as they'd almost always end up in the first one-which means, of course, that there is a bias there. Meanwhile, haven't bothered to use official capitalizations, as it's too much trouble to look them all up. And no, I'm not making links for all those. You can find them yourselves.
Protagonists for Establishment: Akira, Bleach (Shinigami Daikō-hen), Cain Series, Cattō Ninden Teyande~! [sic], Chrno Crusade, Cowboy Bebop, Godzilla, .hack//SIGN, .hack/Tasogare no Udewa Densetsu, Hellsing, Peace Maker Kurogane, R.O.D Read or Die, Rurōni Kenshin (Kyōto-hen, Jinchū-hen), Shin Seiki Evangelion/Neon Genesis Evangelion, Tenchi Muyō!, Uchū no Stellvia, Versailles no Bara, Yami no Matsuei
Protagonists against Establishment: Abenobashi Mahō Shōtengai, Biohazard Code:Veronica, Bleach (Soul Society Kyūshutsu-hen), Blue Drop, Chrono Trigger, Devil & Devil, Dystopia, Escaflowne, Et Cetera, Eternal Arcadia, Final Fantasy IV, Final Fantasy VI, Final Fantasy VII, Final Fantasy VIII, Final Fantasy IX, Final Fantasy X, Final Fantasy Tactics, FLCL, Fushigi no Kuni no Miyuki-chan/Miyukichan in the Wonderland, Grandia II, Hagane no Renkinjutsushi/Fullmetal [sic] Alchemist, Himitsu no Angelis, Hōshin Engi, Kannazuki no Miko, L A S T E X I L E, Loveless, Mahō Kishi Rayearth/Magic Knight Rayearth (first series), Mononoke-Hime, My HiME, My Otome, Ogre Battle, Ogre Battle 64, R.O.D the TV, Rurōni Kenshin (Bakumatsu-hen), Samurai Champloo, Samurai 7, Seiken Densetsu II, Shichi-nin no Samurai, Shimpi no Sekai El-Hazard, Shining Force, Shining Force II, Shōjo Kakumei Utena, Slayers TRY, Super Mario Bros., Tenjho Tenge, Tenshi Kinryōku/Angel Sanctuary, Texhnolyze, Tokyo-under Ground, Top o Nerae!/Gunbuster, Top o Nerae 2!/Die Buster, Yōjimbō, Zelda no Densetsu